Mission
by Juliejo2001
Summary: On a mission to The Space Colony ARK, Shadow and Rouge find more than some missing files. Light AU.
1. Morning

**AN: Well here goes a story I just came up with, due to a very busy school year, I may not update often...**

**Morning**

Shadow The Hedgehog was sleeping in the room he and his partner Rouge shared at G.U.N. HQ. It wasn't anything to talk about, just a bunk bed, a small television, and a dresser they shared. The walls were a dreadful beige color, and they were covered up with papers and pictures and other clues they needed for cases. Other than that the room was blank and bare as the duo were often out on missions, so there was no need to decorate. A large window on the west wall was covered up with pure white curtains, but that did not prevent sunlight from leaking through and waking Rouge up today.

Realizing that her partner was still sleeping, a mischievous grin slowly spread across her face. She quickly climbed down the ladder of her bed, past the empty middle bunk, and to the ground where Shadow slept on the lowermost bunk. She then squat so she was more level with Shadow's face. Shaking Shadow with both arms repeatedly, she whisper-shouted: "Shadow! WAKE UP! WAKE UP! HURRY THERE'S AN EMERGENCY!" She was also trying to hide her large grin as she held back several giggles.

Shadow opened one eye and saw his partner who was laughing so much while doing this and let out nothing more than a "Hmph." He wanted to sleep in as much as possible before the mission they had to leave for in the afternoon and would not let the ivory bat have her way.

Too bad that she continued to try to wake up Shadow even more, causing him to roll over and cover his ears with his pillow. He recalled Rouge saying that she wanted to go for some breakfast at a ritzy cafe, he could remember how she had heard so much about their coffee and their pastries. He also knew that this mission would keep them away for two days at least.

Maybe it was really the mission he was dreading. Not waking up and having to go eat lunch with his companion. A week ago, the G.U.N. Commander had called them over, stating that they'd 'lost' some important files and that the only place they were backed up at was Shadow's old home itself. He didn't really want to go, but he knew that place like the back of his hand and thus he along with Rouge were tasked with investigating the old space station. He had stopped grieving over the lost of his best friend Maria, and while it was fifty years ago, he had only spent two real years awake after being stored in a stasis of sorts. The wound on his heart was healed somewhat, and he'd no longer mope around or the like - but the scar was still there.

Shadow glanced at Rouge for a second, then said: "Fine Rouge, let me go take a bath first." The hedgehog stretched out both arms and let out a hearty yawn. "Go get ready and stuff so we can get to that restaurant. We're not going to wait on a line like last time."

"Yeah, we wouldn't want you to curse a waiter out again." Rouge said snarkily as she regained her stoic, coquette-ish demeanor.

Shadow rolled his eyes at that comment as he tidied up his bunk. Those same irises wandered up to the middle bunk, empty and neat. It was lonely and he secretly wished there was a third member to fill that bunk up.

**A/N: Well there goes the first chapter! **


	2. Breakfast

**A/N: Greetings Pekoponians! I HAVE ARRIVED WITH A NEW CHAPTER! Enjoy, read, review, favorite, what ever is your cup of tea!**

**Breakfast**

Station Square's newest cafe was supposed to be the hottest one there was right now. Right now as in that once the next cafe opened up, this place would become desolate and bare. But right now it was filled with many different Mobians and a few aliens who were stopping at the planet for a chance to relax. It's odd how aliens could secure a reservation as a spontaneous rest-stop if you will. Shadow was stuck pondering that subject for a while, _If we could barely get a table how did those guys get to if they're just passing through? _Shadow once again pondered this and tried to come up with a resolution. However, Rouge noticed this and cleared her throat awkwardly to bring the hedgehog back to reality.

"Shadow. Quit spacing out, the waiter should be here soon." Rouge saw Shadow as a brother, if you will. As in a brother, she meant a _little_ brother. She often had to keep him in line and make sure the gruff and angry hedgehog wouldn't lash out at people for annoying him. When Sonic came over things really got heated and she'd need all her sanity to get through those arguments...

"Huh? Oh yeah. What are you gonna get Rouge?" Shadow said with a bored tone of voice, this cafe would be the death of him. And he's immortal.

A glance around the room they were in showed light baby blue walls with white accenting and picture frames all around it. There were large windows that let the sunlight leak and flood in. Black metal chairs that had twisted-curvish backs with pale-pink cushions. This cafe actually reminded him of Maria. The soft pastel colors she loved, the architecture, pictures surrounding them all. It was almost the exact same way she wished to redecorate her room on the ARK...

Gerald gave in almost immediately - he could not deny his grand-daughter anything. He remembered taking one look at her room and knowing it was his complete opposite. Yet the sweet girl who loved color and light, also loved him. He was dark - quite literally as he was black and red, and had a bit of a grumpy attitude to him. Yet out of all the things like cooking, painting, writing, singing, and studying, she loved being with him the most.

Their differences were completely obvious. The snarky and often irritable Shadow was almost joined at the hip with sweet, innocent, charitable Maria.

Seeing this room made him remember lazy days where they look at the stars and wonder what earth was like, or explore some unknown corridor of the colony, even those times when Maria tried to 'tutor' Shadow in the culinary arts and he'd make the most burnt and horrible tasting meals.

This dish of a hamburger with some bacon however, wasn't one of them. This cafe had delicious food and he actually wanted to come back here some day. Out of the corner of his eye, he saw Rouge enjoying her salad with a smile on her face because they both knew how much this place meant to him now.

After they'd finished their meal, Shadow and Rouge walked over to his motorcycle and sped off and away to H.Q. for their mission.

**A/N: So guys? What did you think? All Sonic characters belong to SEGA and whatnot.  
**

**EDIT: And yeah, Omega's in the G.U.N. labs because he's a robot. He would definitely destroy that bunk DryadPrincess! XD Thanks for reviewing! You too Potato Man!**


	3. Racing Your Rival

**A/N: Well, it's been a long time, here goes! And this story takes place 3 years after the SA2 Sonic X adaption in the same AU as The Best Friends in The World.**

**_G.U.N. Base_**

"Shadow?" Rouge called out as she searched for her partner that just _ditched_ her to go race Sonic for what had been the umpteenth time this week. She let out a loud sigh and crossed her arms. She whirled around to face Omega, who had been in the shop for some repairs. "Look, I don't know when Shadow will get back here, but when he does-" she paused for a moment "if he makes us late for the mission briefing I will never let him see the light of day." She didn't really mean that however, hopefully, for Shadow's sake.

"Affirmative. I shall scan for Shadow to locate him and I shall retrieve him." Omega was about to head for the door but was blocked by Rouge who didn't look enthused in the slightest.

"You're staying here. Tails still needs to fine-tune your upgrades and the last thing we need is for some insane malfunction - like the one that got you in this mess!" Rouge jabbed her finger at the robot who in times of emergency rushed into battle, all units and officers were called out and as one would guess, this was an almost lethal mistake for Omega.

Tails entered the room, "Hey guys, I'm back. I got this super cool weapon idea, what if I tried adding a turbo booster-"

"NO! Go on and finish up repairing Omega so we can start this mission already!" Rouge interjected, causing Tails to practically jump at the outburst.

A bit of exposition is in order here: after the whole Metarex conflict two years prior, G.U.N. decided to recruit the whole Sonic Team, sans Knuckles who insisted that he couldn't be taken away from Angel Island and The Master Emerald, he did assist the group all the same on missions and in cases of catastrophe, so nothing really changed in a way.

**Rainforest -Approx. 15 miles from The G.U.N. Base-**

"You gotta go faster than that to top me Shadow_, or is the Ultimate Lifeform not fast enough to catch me?_" With that remark, you knew Sonic The Hedgehog was definitely tempting fate. But what could be possibly hanging in the balance with this 'friendly race'?

_The loser has to buy lunch._

"Please, I'm holding back. I'll leave you in the dust, _faker._" Shadow retorted as he spin-dashed into some stray badniks that belonged to none other than Dr. Eggman. He rounded a bend and caught the lead as he turned. _One mile left Shadow, and then you gotta get back to base._ Shadow thought to himself as he felt the sticky, warm, tropical air in this small secluded rainforest.

"Oh really? You're holding back? I'm hurt Shadow, you know I expect your A game." Sonic caught up to Shadow, and they were neck and neck.

Only 10 feet to the finish line and a loud _**ring ring**_ erupts from both Sonic and Shadow's wrist communicators.

"Guys can you get back to base? Rouge is losing her patience with you two and she wants Shadow to come over now." Tails then mouthed the words 'help me'.

" 'Kay buddy, hang in there, we'll be back in a cinch." Sonic said, shooting his brother a wink.

"Tell Rouge that she's no fun." Shadow said that in the most dry tone ever known to mankind, or mobiankind for that fact.

"Okay guys. _Please hurry._" The urgency in Tails' voice was hilarious.

**_Space Colony A.R.K: Secret Room._**

The room was dark, dismal. A light hung lazily from the roof, but it stopped working years ago. Several pods decorated and ornamented the room in way, as they lined the walls up and down the long musty corridor.

If one were to squint their eyes they could see past the fog clouding the plexiglass tubes and see them all vacant, empty.

_Except for one._

The figure of a little girl, no younger than 12 could be seen, her chest breathing slowly. She was clothed in a once-blue dress that was now stained with dried up blood. What had been different about this girl now from the time she had been 'killed' was that she, _was no longer human._

**A/N: So we got a bit of world building and a bit more character interaction, and a nice little teaser about Maria. Good work today me! *Pats my own back* I should update more regularly now that I got out of this little case of writer's block. PLEASE READ, REVIEW AND COMMENT!**


	4. Shock

**A/N: Here we go! It's almost time to meet MARIA!**

**/\/\/\/\**

**Space Colony A.R.K. - Main Corridor**

Shadow let out a grunt as he traversed the dimly lit, lengthy hallway. If he closed his eyes and tuned out Rouge's incessant rambling about whatever it was that troubled her, he could almost see all the scientists that used to work here going about their daily lives. It would seem almost the way it was years and years ago. He most certainly - without a doubt in the world - could see Maria staring quietly out the window, wishing and yearning for more. Praying to have a normal life and to live on Earth like most twelve year old girls do. He saw her cheery smile and pale features, blond hair that would flow freely-

"Shadow?" A feminine voice that was especially irritated rung out. It called his name again, finally snapping him out of his trance.

"Yeah?"

"I'm going in to get the files. Are you okay- _Shadow!_ Are you daydreaming?" Rouge was tapping her foot repeatedly on the linoleum, it was very loud and it clearly depicted her mood as of late. She was getting tired of Shadow spacing out and thinking about Maria. They had a mission to worry about! She understood that he missed her but it still was no excuse for being so unprofessional on the job.

"No. I'm fine, just go in and get this whole information-recovery thing started." He replied gruffly, but deep down he knew she was right. He's always so focused on the task at hand - but this task, this very mission they were given was too painful for him. There wasn't some evil overlord who had to be stopped, no revenge, _no nothing_. This was all about some stupid files. He continued, "I'll double back and check on Omega. Just to make sure the Doctor didn't leave some stray badniks or an E-Series robot nearby. Omega would wreck this place if that happened."

"Fine Shadow. Go and do that." Rouge regained her composure and strutted away.

**/\/\/\/\**

**Space Colony A.R.K. - Left Wing**

Shadow tried his best to walk as quietly as possible - this was hard with his skates on, but he managed to make do. One loud noise and a plethora of traps would be triggered. Now, of course the scientists on the Ark wouldn't rig up one of their main wings - but Robotnik did when he had taken over the Ark in an attempt to use it's Eclipse Cannon to terrify the citizens of Earth into giving in to his "Eggman Empire".

Shadow was of course ashamed to have been part of such a stunt, but one benefit of having been associated with this plot was knowing where _not_ to step. His and Rouge's knowledge of the Ark and the location of the remaining traps and E-Series robots would help in this mission to clear out the premises.

As he continued to traverse this hallway, he heard a loud noise. It was almost like a piece of large metal hit the floor.

Shadow, naturally braced himself for any death trap or mech that might await him. Of course, he was indeed immortal. But he could still feel pain. And then if a killer robot appeared, Rouge could get hurt. And Omega would most likely cause mass destruction as his 'primary objective' was to destroy the remaining E-Series robots and prove himself superior.

Thankfully, nothing happened. Shadow took a quick look to his right, where the noise most likely came from. When he realized what this meant, his heart sank.

_He'd have to enter Maria's old room._

Painful memories tore through him as he saw the dusty and dirty state the bedroom was in. It felt like it was just yesterday when they used to spend so much time in each other's company. He sat down on her bed and buried his face in one of his hands and let out a sigh.

Suddenly, he noticed he was sitting on something. He shot straight up and noticed her old diary was there, under the sheets. He stood there in disbelief for a moment.

Cautiously lifting the sheet up, he could only make out one word G.U.N.- before another startling **_crash_** erupted. He bolted to his left and pressed his hand against the wall. Quickly, he felt it for any false walls or hidden doors.

It was only mere moments until he found it, and using the super strength that would come with being _The Ultimate Life Form_, he was able to reveal a hallway.

He walked down the hallway, it was lit, surprisingly - the A.R.K was over 50 years old. He came across a metal door labeled _**TOP SECRET.**_

He opened the door, twisting the knob to the right to find it was locked. He gave it a ferocious tug and it gave way with a lound banging noise as it touched ground. He saw large tubes that were fogged up and empty.

The center pod was broken, shattered glass surrounding it. He walked up to the remnants and found some files on the ground and a swatch of blue fabric.

He stared at the cloth for an undetermined amount of time until he finally resolved to thumb through the files.

All that was there were some overly technical reports that didn't really hold his interest. And a profile with a picture atrached to it. After dusting it off, Shadow was in for a surprise. The picture was of none other than his departed friend Maria, and one line in particular that caught his attention.

**_Subject Status: Medically-Induced Cryogenic Coma_**

_"What the hell..."_

Shadow glanced upwards to see tubes and wires hanging from the apparatus. He was in a state of complete shock. And then it hit him: Maria is alive. And if they think they can take her away from him again, they had another thing coming.

**A/N: DUN DUN DUN! It's gonna go down next chapter!**


	5. Reunion

**A/N: Okay no more procrastination! IT'S TIME! (Dun dun dun) **

**Also, I just realized I have to say that ALL CHARACTERS BELONG TO THEIR RESPECTIVE OWNERS AND THAT THIS IS NOT FOR ANY FINANCIAL GAIN.**

**/\/\/\/\**

S**pace Colony Ark - Right Wing**

The young girl's breathing was labored as she ran throughout the empty hall. She had no idea she could run _this_ fast before, but she also wasn't a Mobian beforehand either. The sudden transformation that she discovered would have shaken her to her very core, but one thing kept her running throughout this ghost station.

"S_hadow. I need to find him and stop him before it's too late."_ She thought intensely to herself, replaying her memories over and over again as she ran further and further away from the place where she'd awoken.

She _couldn't_ have told him to get even with everybody else. She didn't say that. "I c-couldn't have." She stared at the floor as her run came to a stop.

Placing her hand against the glass, she could see a hedgehog looking back at her. That wasn't her - it couldn't be her. She looked so different, and her memories were most certainly different. Just as she was going to break down, she remembered Shadow.

Maria took off again, looking for her friend, unaware that she was trying to prevent a disaster that was already averted.

**/\/\/\/\**

**Space Colony Ark - Secret Room**

Shadow was in a complete daze as he stared at the files; the fabric; the broken glass. He blinked quickly and tried to make sense of this all. _Maria was alive. She was alive. Not dead._

Shadow quickly turned around as he noticed a giant hole in the wall. A mine probably caused the giant _bang_ he heard earlier. Yet this answer brought up a new question: _Why woupd Eggman place a mine here?_ Picking up the folder, he cautiously thumbed through all the information.

Maria's own DNA was apparently transfused with some hedgehog DNA and given some Black Blood the night before the raid. And then a personal note from Gerald was attached to this.

_I can't let Shadow or Maria know this. If G.U.N. thinks they can halt this project and kill all onboard, they and the rest of the world will be punished. Those who threaten my family will suffer. In the case of my capture, I have already set up Shadow and Maria so that their memories of the incident will be different and they can get my revenge._

This was most certainly an interesting development for Shadow. He simply placed all the files inside the folder and rung Rouge up on his wrist communicator.

"Rouge. I found some files that weren't backed up. Be on the lookout for a girl okay?"

"A girl? Here?"

"Yes. And call up Omega as well. I have to investigate something. A mine blew up a wall and caused a mess in the room the girl was supposed to be in."

"Got a description of her?"

"No. I know it sounds crazy but I think it might be..."

"Shadow. She's gone." Rouge's voice was somber.

Shadow's lips curved into a smirk. "Check out the files, I'll scan 'em over here and you'll see who this girl is."

"What-" A splitscreen opened up on the communicators as the files were on the communicator. She read it quietly and yhen continued. "This is some freaking miracle. But what about her memories? If she isn't anything like how you were when you woke up I bet she's definitely scared shitless."

"More of a reason to find her. Meet up at about 17 hours?"

"Five. Got it."

After the call Shadow inspected the metal that was curled up and decrepit. His ears perked up as he heard footsteps and a soft voice crying not far ahead. He bounded down the right wing thankfully, the doctor didn't put many traps here so Maria probably wasn't injured or hurt.

He saw her right there, sitting on the floor in a confused heap with her shoes that were too small now beside her. She looked so different, yet so familiar at the same time. She was even a bit... beautiful and this thought made Shadow stand there in awe. He realized that Maria was staring back at him now and she was a little red-faced.

He walked over to her and fell on his knees beside her with a joyful look on his face. He wrapped his arms around her and cried tears of joy, sniffling as his grip on her waist didn't falter.

"Shadow... Please stay here. Don't do what I said, I don't know why I'd do that-"

"Shh. It's okay. I know you wouldn't do that. The world's become more confusing than before and what happened in the past can wait for later. I'm just glad you're here again." He softly stroked her back and buried his face in her hair-in her quills. Yeah.

"Here again?" She blushed lightly as she nuzzled closer to his body.

"Here in my arms again." He began to lean in closer to her lips, blissfully unaware of what he was doing until...

"Objective not accomplished. Shadow is in the vicinity and has Maria. Shall I chauffeur you?" Omega barked out as Shadow nearly peed on himself in fright. Maria gasped in confusion.

"Y-yeah Omega." Shadow walked over to Omega and didn't let go of Maria's hand.

She took notice of this and smiled softly to herself, _"It'll be okay. As long as I have Shadow I'll be safe."_

Too bad that she triggered one of the only mines in the hall and a ticking noise could be heard. Shadow's eyes widened in shock and hoisted Maria up bridal style. He nodded at Omega to kick it into over-drive and run.

The ticking became louder and louder, and Shadow's worst fear manifested itself - the deadliest bomb on the A.R.K. was activated. He knew it was on the ship but he never thought it would be here. Just as it was about to blow and Shadow thought it would be the end, Rouge grabbed both him and Maria and got them out of the way just before the ensuing blast.

"The Commander is gonna _kill_ us." Rouge said quietly.

"Affirmative." Omega croaked out.

**A/N: Hoooo boy we are just getting started with this. It is going to get pretty action packed soon. After some more Shadaria fluff that is. :D**


End file.
